Doctor Dee was a confidante of Elizabeth I, a mathematician and alchemist. Damon Albarn has written an opera about him and says the work has allowed him to express his patriotism

It’s Tuesday morning in the mess of glass, metal and international retail brands that is modern Manchester, though Damon Albarn has arranged to meet me somewhere very different. Just across the road from the city’s Victoria station is Chetham’s Library – the oldest public library in the English-speaking world, and a place once frequented by Karl Marx. Inside its reading rooms, there is a beautiful hush.

Albarn, currently sporting a thick beard, is here in connection with someone currently much on his mind: John Dee, the confidante of Elizabeth I, mathematician, navigational pioneer, alchemist and supposed magician who served as the building’s warden for 10 years at the end of the 1500s, when it was an adjunct of the nearby cathedral. By this time, having blazed an intellectual trail across Britain and Europe, Dee was at the end of his life, with plenty of controversy and emotional wreckage behind him. One biography sums up his presence in Manchester as a matter of “virtual exile, placing him far outside the orbit of the Queen and her court”. His existence here seems to have been forlorn and unproductive, and made yet more wretched by the death of Elizabeth in 1603. He returned to London two years later, but lived for only another three years – though at 82 he hardly died young.

Now, Dee’s ghost has returned to Manchester in rather more favourable circumstances. Albarn and the director Rufus Norris have built an “English Opera” entitled Doctor Dee around his story, which will be premiered as part of the Manchester International festival on 1 July. On the other side of town, a company of actors and dancers is deep in rehearsal, while elsewhere the BBC Philharmonic Orchestra is perfecting the score – any time now, they will be joined by a core of musicians, including Tony Allen, the 70-year-old Nigerian drummer whom Albarn credits with a “cosmic pulse”. Albarn himself will take an onstage role – delivering, he says, songs that draw lines between Dee’s time and our own, centred on “relationships, religion, hedonism, the reinvention of ritual . . . and politics, a little bit. There’s a lot going on.”

To make things even more interesting, the production is intended to evolve as it’s rehearsed and performed, which partly explains Albarn’s visit to Chetham’s library: when the chief librarian appears with a handful of books once owned by Dee and strewn with his annotations, Albarn reaches for an A4 notebook, and scribbles down at least one line he seems to think might help him with a lyric. “This isn’t like making a record,” he says. “It changes. And when we present it on that first night, it’ll still be in a state of flux.”

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Alchemy and court intrigue, the linking of two Elizabethan ages, and music that fuses no end of influences: as the Guardian’s music critic Alexis Petridis put it in 2007, “to think Albarn was once compared unfavourably to Liam Gallagher . . . These days, that seems a bit like comparing David Bowie to Les Gray of Mud.”

The range of his recent(ish) work is dazzling. In January 2007, Albarn released The Good, The Bad and The Queen, created by a band including Tony Allen and the former Clash bassist Paul Simonon, and sprinkled with the same English mysticism that the music from Doctor Dee evokes. Later the same year, there was the premiere of Monkey: Journey to the West, the work of Albarn, the artist Jamie Hewlett and the Chinese actor and director Chen Shi-Zheng. In 2009, Blur temporarily reformed, crowning their return with a performance at Glastonbury; and in 2010, Albarn released the third album by his ongoing pop project Gorillaz, featuring, as always, Hewlett’s artwork. And now there is this – his bravest step yet away from the musical mainstream.

The genesis of Doctor Dee dates back at least two years. Alex Poots, the Manchester festival’s director, had approached the writer and graphic novelist Alan Moore with a view to involving him in a stage production, and Moore’s passionate interest in Dee led to a meeting with Albarn and Hewlett. Albarn had already begun to think about working on an unspecified “heartfelt English piece”, and learning about Dee’s story hardened his resolve – but Moore and Hewlett then dropped out, leaving Albarn in charge of the project.

“I knew I had a fascination with aspects of history that were slightly more esoteric,” he tells me. “I enjoyed history at school. I’d always had a sense of Pagan England. I have very clear memories of getting caught up in a TV series about Robin Hood when I was a kid. And I can remember having a strong sense of imagery from an old monastery in Sussex, near a house we were living in for the summer. This is all a personal thing: my relationship with these aspects of being English. But this story had so many catalysts: it didn’t seem like it would be too mad an idea to start thinking in musical terms.”

“I do harbour this feeling about my country, and it doesn’t come out that often, because I’m off doing other things,” he goes on. “Which is great, because that way, it gets stronger, and it’s nice to wait till it really needs to come out. So this is more than something I’m doing for a festival. It’s been brewing for ages, trying to find its essence.”

Albarn’s first source of information was The Queen’s Conjuror, a much-praised biography of Dee by Benjamin Woolley, published in 2001. “That showed me how little I knew,” he says. “The references go all over the place. So I began to say, ‘Well, this month I’m going to be reading up on hermetic tradition. Then cabalism, and then Celtic pagan tradition, then the origins of Christianity.’” He says he’s still ploughing through a mound of reading that may take five years to complete; the latest book is The Night Battles, an account of witch-hunts in Europe in the 16th and 17th centuries by the Italian historian Carlo Ginzburg.

Drawing one central storyline from Dee’s incredible story looks almost too challenging. His life moved from London, to Cambridge, to Belgium, on to the Elizabethan Court, and in turn to Central Europe. His range of expertise was extraordinary, in an era just before science and the occult began to be disentangled. Dee has been credited with the first use of the term “British Empire”; he certainly insisted that England had a legitimate claim to North America, and argued that territorial expansion had to be led by a navy. His story intersects with those of such major Elizabethan figures as Francis Walsingham and Walter Raleigh; he is also believed to have been the inspiration for Prospero in The Tempest, and possibly for Marlowe’s Doctor Faustus.

So where to start? Two weeks before my visit to Manchester, as various rehearsals take place around Albarn’s HQ in west London, I talk to Doctor Dee’s director, Rufus Norris. Part of the plot, he explains, turns on Dee’s meeting with Edward Kelley, a mysterious figure said to be one of the Elizabethan period’s itinerant “skryers” – self-styled seers and psychics. The pair began supposedly communicating with spirits, and then angels – who, Dee claimed, dictated no end of material to him in their own “Enochian” language, which he transcribed using odd symbols somewhere between runes and Greek letters. Unfortunately, Kelley’s chief impact on his life was not nearly so other-worldly.

“It could be argued that in Britain, if not in Europe, Dee knew more than anyone else,” Norris says. “And yet he screwed up when it came to the most simple imperative – to look after the thing that’s closest to you. In their last consultation with spirits, Kelley gave him the message from God that they should share their wives. And everything fell apart from there. So in terms of how you find a narrative . . . well, the man learned a huge amount, he searched for more, and that search took him out on a precipice, and he fell off the end. It’s a tragedy.”

The songs that tell the story draw subtly on Elizabethan music, but also, thanks to Allen, on more unorthodox elements. Doctor Dee’s core arrangements are built around organ, harmonium, drums, acoustic guitar, a harp-like Malian instrument called the kora – and such European instruments as the viol and theorbo, the latter a lute-like instrument with a long neck. The music is elegant and full of a sense of warmth and intimacy. In west London I watch a piece called “Godfire” taking shape, intended to suggest both the coronation of Elizabeth I and the recent royal wedding – a reference that might make at least some of Albarn’s admirers a little uneasy (in 1997, he turned down an invitation to one of Tony Blair’s Downing Street soirees, claiming he was “now a communist”). Alluding to the wedding’s ceremonial fly-past, its opening line runs thus: “Hurricanes, spit and Tornado, growled over London today.” In Albarn’s telling, the song reflects the almost subconscious sense of nationhood that sits at Doctor Dee’s heart.

“It was strange,” he says. “That day, I was up at the top of my studio. My daughter and her mates wanted to watch the wedding there, because the studio has a big TV. So we were watching it, and I was also watching the fly-past happen outside. I’d just heard ‘Jerusalem’, and there were trees in the Abbey . . . I was moved.”

I say that he doesn’t strike me as a monarchist. “I’m not a monarchist. But I’m English. And I have an irrational emotion for my country.”

Next year, Doctor Dee will play at the London Coliseum, as part of the Cultural Olympiad. Once its Manchester run ends, Albarn is travelling to Congo, to play his part in a project in which DJs and producers will record and sample Congolese music, and aim to complete a record in not much more than a week. Blur, he says, may reunite again, to play their old songs in the US, though when I ask him about the possibility of new Blur songs, I get a mumbled “don’t know”. There is also final work to be done on a largely instrumental album made by Albarn, Allen and the Red Hot Chili Peppers bassist Michael “Flea” Balzary.

And then? I ask him the question in west London, just after he and the musicians have run through another song. Albarn’s face breaks into a smirk. “Oh, something that’s the opposite of this. The most cheesy pop record ever.”

The world premiere of Doctor Dee: An English Opera is at the Palace Theatre, Manchester International festival, 1-9 July 2011. For more details visit mif.co.uk